Modified melamine cyanurate (M-MCA) obtained through molecular complexation was used to flame retardant polyamide 66 (PA66). The investigations showed that M-MCA flame retarded PA66 was self-extinguished quickly and there was non-flammable melt-drips. During the vertical burning test,the system achieved V-0 rating (1.6 mm) at 8 % M-MCA loads, and also gained good mechanical performances. Thermogravimeric analysis (TGA) and microscale combustion calorimetry (MCC) were conducted to investigate the combustion behavior and the corresponding flame retarding mechanisms of M-MCA flame retardant PA66.